def createOutputData( jobs ):
""" Reads out the meta data.
"""
failedImages = []
nJobs = len( jobs )
for n, j in enumerate( jobs ):
print( "Job " + str(n+1) + "/" + str( nJobs ) )
# load every image
metadata = []
nImages = len( j.sourceImages )
nChannels = -1
for m, img in enumerate( j.sourceImages ):
print( "\tReading image " + str(m+1) + "/" + str( nImages ) )
imgPath = os.path.join( j.sourcePath, img )
options = ImporterOptions()
options.setId( imgPath )
options.setSplitChannels( False )
options.setWindowless( True )
options.setVirtual( True )
imps = BF.openImagePlus( options )
if len(imps) == 0:
failedImages.append( imgPath )
print("t\tCould not load image: " + imgPath)
continue
# get the meta data
data = imps[0]
if nChannels == -1:
nChannels = data.getNChannels()
imgInfo = Info();
info = imgInfo.getImageInfo( data, data.getChannelProcessor() )
metadata.append( imgPath )
metadata.append( info )
j.outputData = '\n\n>>> next source file >>>\n\n'.join( metadata )
j.numChannels = nChannels
# @File(label="Input file") input # @File(label="Output folder") output # Splits multi-point CZI files into multiple TIFFs using Bio-Formats. # # Stefan Helfrich (University of Konstaz), 05/09/2016 from ij import IJ from loci.plugins import BF from loci.plugins.in import ImporterOptions import os srcPath = input.getAbsolutePath() # using LOCI BioFormats settings = ImporterOptions() settings.setId(srcPath) settings.setOpenAllSeries(True) settings.setVirtual(True) settings.setWindowless(True) imps = BF.openImagePlus(settings) for i in range(0, len(imps)): currentImp = imps[i] filename = os.path.split(srcPath)[1] filenameWithoutExtension = os.path.splitext(filename)[0] IJ.saveAs(currentImp, "TIFF", output.getAbsolutePath() + "/" + filenameWithoutExtension + "-" + str(i) + ".tif")
